[gmx-users] some hardware questions

(and another work about it). And are there bigger differences (if someone knows) in use 1 Gbps onboard NIC vs. better? add-on NIC cards e.g. Intel Pro/1000 CT or similar? In MPI calculations with use 4 to 8 cores per computing node. Thanks a lot. Milan Melichercik -- gmx-users mailing listgmx

Re: [gmx-users] Size of generating data

On Tuesday 20 April 2010 18:02:50 Bharath.K. Chakravarthi wrote: hi all I'm running simulation for a protein of about 150 amino acids for 100 steps i.e 2 ns in a system of about 35 GB disk space. is there any way to know the approximate size of generating data. The grompp

Re: [gmx-users] about g_sas analysis

supti mukherjee wrote: Dear gromacs users, I have some doubts regarding the options to be selected in g_sas program. g_sas asks for two groups, first one for calculation and second one for output. As I have understood from the manual that first group should contain all non solvent groups and

Re: [gmx-users] g_bundle problem

On Friday 19 March 2010 02:36:49 Stefan Hoorman wrote: I have tried using g_bundle in order to analyse helix axes in my transmembran helices. I created two groups in my ndx file that included the alpha carbons of the first half of my helix and a second group for the alpha carbons for the

Re: [gmx-users] Extending simulations

On Wednesday 17 March 2010 13:53:03 Carla Jamous wrote: Hi everyone, It's the first I use the process of extending simulations. I did the following: tpbconv -s prot.tpr -extend 6000 -o protein.tpr mdrun -v -s protein.tpr -cpi state.cpt -cpo state_a.cpt -o protein.trr -c protein.gro -x

Re: [gmx-users] Gromacs commercial license

On Wednesday 27 January 2010 19:40:57 Guilherme Menegon Giesel wrote: Hello folks!! Does anyone know if there is a GROMACS version to commercial use, or under somekind of license? If so, how should I proceed to get such license? Best regards!! Gromacs is under GPLv2 license

Re: [gmx-users] Restarting a gromacs calcluation

Dňa Pi 16. Marec 2007 14:19 Triguero, Luciano O napísal: Dear Users, Thank for your help. I started a 10 ns simulation, but it dies because of an error in the cluster PBS system, so I want to continue the simulation from the last (r,v) point. May I still use tpbconv to restart from that last

[gmx-users] radial densities

Hi guys, maybe I ask stupid question and I missed something, but I want to compute radial densities (perpendicular to an axis of a alpha helix peptide), but I couldn't find suitable program to do this job. Thanks a lot for help Milan ___ gmx-users

Re: [gmx-users] protein in bilayer

Dňa St 23. August 2006 13:42 mahbubeh zarrabi napísal: dear itamar where is adress make-hole site? thanks 3rd record on following page http://www.gromacs.org/contributed_by_users/task,cat_view/gid,24/dir,DESC/order,name/limit,5/limitstart,5/ ___

Re: [gmx-users] Precision between 32 and 64 bits machines.

Dňa Ne 30. Júl 2006 01:47 zazeri napísal: The precision of Gromacs compiled for single precision on 64 bits machine is equal to precision of Gromacs compiled for double precision on 32 bits machine ? AFAIK no. The single precision is 32bit floating point number, double is 64 bit - on ALL